SMTL ID : 9fmr.1

Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.90 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 x RMF: ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine(Non-covalent)

RMF.1: 21 residues within 4Å: Chain A: N.631, R.652, R.671 Chain B: I.21, G.22, E.23, V.29, A.42, V.75, F.101, E.102, Y.103, M.104, D.105, H.106, D.107, M.109, S.151, L.154, A.164, D.165 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.21 Hydrogen bonds: B:E.23, B:Y.103, B:M.104, B:M.104, B:D.107, B:D.107, A:R.652 pi-Stacking: B:F.101 pi-Cation interactions: A:R.652 RMF.2: 21 residues within 4Å: Chain D: N.631, R.652, R.671 Chain E: I.21, G.22, E.23, V.29, A.42, K.44, V.75, F.101, E.102, Y.103, M.104, D.105, H.106, D.107, S.151, L.154, A.164, D.165 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:I.21 Hydrogen bonds: E:E.23, E:M.104, E:M.104, E:D.107, D:R.652 pi-Cation interactions: D:R.652 RMF.3: 20 residues within 4Å: Chain G: N.631, R.652, R.671 Chain H: I.20, I.21, G.22, E.23, A.42, V.75, F.101, E.102, Y.103, M.104, D.105, H.106, D.107, M.109, S.151, L.154, A.164 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:I.21, G:R.652 Hydrogen bonds: H:E.23, H:M.104, H:M.104, H:D.107, G:R.652

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anand, K. et al., Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835. To Be Published

Release Date

2024-10-16

Peptides

DNA damage-binding protein 1: ADG
Cyclin-dependent kinase 12: BEH
Cyclin-K: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

B
B

E
E

H
H

C
C

F
F

I
I

DNA damage-binding protein 1

Cyclin-dependent kinase 12

Cyclin-K

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